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Number 12

Jul 2014

PHOTOGRAMMETRY IN PALEONTOLOGY A PRACTICAL GUIDE

Heinrich Mallison1 & Oliver Wings1,2


1- Museum fr Naturkunde Berlin, Invalidenstrae 43, 10115 Berlin, Germany.
2- Niederschsisches Landesmuseum Hannover, Willy-Brandt-Allee 5, 30169 Hannover, Germany.
Emails: heinrich.mallison@gmail.com (HM), dr.wings@gmail.com (OW)

ABSTRACT

Photogrammetry is increasingly becoming the gold standard for surface digitizing in paleontology. We present
techniques for specimen handling, photography and image handling in photogrammetry software that are specially
adapted to typical use cases in paleontology, but are also applicable in other science disciplines like archaeology
and art history.
keywords: Photogrammetry, 3D-model, handbook, how-to

RESUMO [in Portuguese]

A fotogrametria est a tornar-se a tcnica standard para a digitalizao de superfcies em paleontologia.


Apresentamos vrias tcnicas para o manejamento de espcimes, fotografia e processamento de software de
imagem que est especialmente adaptado a casos tpicos em paleontologia, mas tambm aplicvel noutras
disciplinas cientficas como a arqueologia e histria de arte.

How t o cit e t his art icle: Mallison, H. and Wings, O., 2014. Phot ogrammet ry in paleont ology a practical guide. Journal of Paleontological
Techniques, 12: 1-31.
Copyright (c) 2014 by Mallison, H. and Wings, O. This work is made available under the terms of the
Creative Commons Attribution 3.0 Unported License, http://creativecommons.org/licenses/by-sa/3.0/.

www.jpaleontologicaltechniques.org

ISSN: 1646-5806

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


INTRODUCTION

Digital three-dimensional (3D) models continue


to revolutionize paleontology. They allow
archiving, analyzing, and visualizing specimens
that would otherwise be difficult or impossible
to access, and can protect delicate specimens
from handling. Many methods exist to create
3D-datasets, such as laser scanners, reflective
light
scanners
or
computation
from
tomographic
data
sets,
e.g.,
computed
tomography (CT) scans. For an extensive
review of current methods see Sutton et al.
(2014).
Over the last few years, photogrammetry has
revolutionized the digitizing process for surface
topography. The process involves taking a
series of photographs of an object from
different angles to computationally generate a
3D model by comparing features across the
photographs. Incidentally, Sutton et al. (2014)
recommend photogrammetry as the first
method of choice for all surface-only 3D
digitizing. As a proven and affordable
alternative to laser or structured light scanning,
photogrammetry is increasingly becoming the
method of choice for paleontological research.
Done correctly, it not only delivers highly
accurate and (if so desired) textured models,
but is also user-friendly, relatively fast and
inexpensive. Here, we provide a simple
introduction to the practical application of
photogrammetry for paleontology and other
specimen-based research disciplines dealing
with specimens in the centimeter-upward
range.
Applications for photogrammetry involve many
different fields, including topographic mapping,
engineering, manufacturing, quality control,
architecture,
movie
production,
police
investigation (i.e., collision engineering, crime
scene documentation), archaeology (e.g. De
Reu et al. 2013), meteorology as well as
geosciences.
Depending on the photographic method used,
the
potential
maximum
resolution
of
photogrammetry varies considerably. At the
extreme, scanning electron microscope (SEM)
photographs can be employed to create models
at nanometer resolution (Piazzesi, 1973;
Kearsley et al., 2007). The typical usage in
paleontology involves consumer to high-end
professional DSLR cameras. The resolution of a
model depends on the resolution of the sensor
and the distance between the sensor and the
object. High-megapixel DSLRs allow creating
models with a resolution measured in tens to
hundreds of micrometers. Falkingham (2012)
found that even a camera with only 8

2 Journal of Paleontological Techniques

megapixels allowed him to produce models with


an accuracy significantly better than 0.3 mm.
Because the data capture for photogrammetry
is usually performed via a conventional DSLR
camera, the method is very versatile and
mobile. Taking photographs is usually possible
in practically any place where paleontological
specimens are located, be it the field, collection
rooms, or exhibitions. Direct physical access is
not required (although it often is helpful), and
given the ability to use a tripod and a suitable
telephoto lens even specimens that are far out
of reach can be digitized satisfactorily for most
research purposes.
Here, we present techniques for photography
and image handling in photogrammetry
software that are adapted for typical use cases
in paleontology. Naturally, they can be applied
to other fields of research as well, including
e.g. archaeology and art history, as long as the
specimens
of
interest
are
similar
to
paleontological objects.
How does photogrammetry work?
Photogrammetry, or more strictly speaking
stereophotogrammetry, is the derivation of 3D
information on points, lines and areas on
objects or terrain from photographic image
sequences. It is a non-contact technique which
creates virtual reality 3D scenes with real-life
textured models. Created data can be used for
measurements and interpretation of objects by
providing precise 3D point coordinates and
other
geometric
and
semantic
object
information
such
as
size
and
volume
information. It can be used in digital, graphical
and orthophoto forms as maps, charts and
overlays, but also 3D-printed to create precise
copies of the original objects.
As of spring 2014, there are more than 40
different computer programs available that are
capable of creat ing phot ogrammet ricmodels
(e.g.,see.https://en.wikipedia.org/wiki/Compari
son of photogrammetry software). Cost-free
programs include VisualSFM (Wu, 2007, 2011;
Wu et al., 2011) and Autodesk's 123D Catch
(however, the latter can be used free of
charge, but the fine print says that Autodesk
actually owns any scans you make and can use
it for a wide variety of purposes, including
marketing). We present our examples with the
commercial
software
Agisoft
Photoscan
Professional (www.agisoft.ru), which we believe
to currently be one of the most user-friendly
programs for photogrammetry. However, it
must be noted that Photoscan Pro offers
comparatively little options for user control. In
the context of the methods presented here, this
limitation does not matter, as we expect

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


readers to be able to produce photographs that
do not result in the necessity to fine-tune and
tweak the program input. If, however, older
photographs without EXIF data or other
problematic data sets are to be used, other
programs may be better suited to the task.
Advances in technology and the software
development in photogrammetry are still very
rapid and have resulted in vastly improved
accuracy and user-friendliness in recent years.
It is likely that some aspects of our guide will
become obsolete through future technological
and software improvements. For example,
Falkingham (pers. communication April 2014)
found that between his submission of
Falkingham
(2012)
and
its
publication,
photogrammetry methods saw a speed
increase of ~10-100x models that had to be
done over a couple of days can now be done in
an hour or so. However, we believe that the
majority of our suggestions for photographic
procedures will always help in creating a clean
dataset of paleontological objects.
Photogrammetry strongly depends on the
source data material and is a good example for
the GIGO principle (Garbage In, Garbage
Out). On one hand, if the photos are not of
good quality, they limit the quality of the
resulting 3D model, no matter how good the
software is. On the other hand, with good
source photos, one can always reprocess the
images with an updated version or a different
computer program at a later time. Essentially,
photogrammetry is about taking good photos
with some differences to normal photography
work. However, this does not mean that useful
3D models cannot be obtained from low-quality
photographs, or images taken without the
intent to use them for photogrammetry. In
fact, as long as several images from different
viewpoint exist, models can be created. An
exciting example of photogrammetric modeling
in paleontology from old images is the
reconstruction of the famous Paluxy River
sauropod and theropod dinosaur trackways
from
12
photographs
taken
in
1940
(Falkingham et al., 2014).
The actual process of creating a 3D model from
photographs starts with the program using,
e.g., the SIFT algorithm (Lowe, 1999) to find
specific points on each image. In the next step,
points from all images are compared to each
other, with the aim to find corresponding image
parts. This so-called correspondence problem
(https://en.wikipedia.org/wiki/Correspondence
_problem) is often solved using the RANSAC
algorithm (Fischler and Bolles, 1980), which
simultaneously also calculates the fundamental
matrix.(https://en.wikipedia.org/wiki/Fundame

3 Journal of Paleontological Techniques

ntal_matrix_%28computer_vision%29)
that
defines mathematically how the image parts are
related. SIFT and RANSAC are also used for
panorama stitching (Brown and Lowe, 2007), for
example
in
the
free
software
hugin
(http://hugin.sourceforge.net). The output of
this step is called a sparse point cloud,
consisting of the 3D coordinates of those points
that were used to align the images. Because
alignment does not require the use of all
available points in high resolution images,
typically only a small percentage of points are
used to keep the calculation times tolerable.
In the next step, all points are used to create a
high density point cloud, termed dense cloud,
that is a very close representation of the real
physical objects in the photographs. This cloud
can then be turned into a polygon mesh or
polymesh which consists of triangles that
connect the points. Color information can be
included by directly taking the color of the
various points from the photographs or by
separately calculating a texture for the mesh.
Figure 1 shows a diagram of the work process
with a recommended workflow.

PHOTOGRAMMETRY IN PALEONTOLOGY
In paleontology, the most common use of
photogrammetry is the three-dimensional
digitization of specimens. Previously, the
complexity of the required calculations allowed
only the measuring of individual points (e.g.
Gunga et al., 2008), not entire point clouds.
The massive increase in computing power and
advances in programming during the last
decade, however, have made such limited
forms of data collection outdated. Research
areas of interest are mainly biomechanics,
including locomotion, ranges of motion and
body mass, or the reconstruction soft tissue
volumes, as well as morphometric studies and
ichnology. Removing the necessity to handle
heavy, fragile and rare fossil specimens for
research, digital models allow computer
simulations which widely expand possible
research topics. Immobile or very heavy
specimens often require significant effort and
expenses to study, whereas the ease with
which a high-detail 3D model can be
transferred, viewed and measured makes them
accessible to practically everybody. Also, scans
do not decay, whereas real fossils can be
damaged by exposure to the elements or
during research. A major advantage of using
digital files is the ability to simply save any
configuration of many objects at any time, and

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 1: Workflow diagram. Red steps are minimum work path for production of dense point cloud and polymesh final
output. Orange steps are highly recommended for any kind of specimen. Blue steps are additionals for multi-chunk use or
one-chunk method with several photo sets. Green steps are additional in-program work to salvage data sets that do not
work out well. Bold blue arrows mark regular minimum-effort workflow.

4 Journal of Paleontological Techniques

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


to compare various configurations directly to
each other, all without any risk to the actual
physical specimens.
The documentation of excavation progress and
the exact geospatial relationship of fossils
and/or sites can be accurately recorded. Maps
of fossils in the quarry can then be produced at
high accuracy with ease, and if several series of
photographs are taken at different times, the
maps can be produced even as 3D maps that
show the vertical arrangement of the fossils
including exact distances.
Aside from musculoskeletal modeling (e.g.
Hutchinson et al., 2005), paleoichnology, the
study of fossil tracks, is the research area that
can probably profit the most from the
availability of a rapid, versatile, field-suited and
highly accurate 3D digitizing method, i.e.
photogrammetry.
The
application
of
photogrammetry to fossil tracks had indeed a
pioneering role in paleontology (e.g. Matthews
& Breithaupt, 2001; Matthews, 2008). Many
tracksites are physically inaccessible during
certain times of the day or year (e.g., covered
by water in the intertidal zone, in rivers and
lakes). Tracks which are otherwise affected or
even destroyed by weathering and erosion
because they cannot be excavated due to size,
location or other reasons can be documented
and the data preserved. In fact, Adams et al.
(2010) suggested that digitypes, digital
holotypes, should be introduced for that very
reason. Digital track models are far easier to
compare with existing data and represent an
objective dataset, virtually not influenced by
interpretation. For example, the often-used line
drawings of track fossils can differ significantly
for the same track if done by different
researchers (Bock, 1952: plate 44).
Workflow
The
workflow
of
photogrammetry
in
paleontology consists of two or three main
parts:
1. Photography
2. Image editing (may not be necessary)
3. Model calculation
Model calculation itself consists in principle of
the following steps:
1. In-program data setup (includes scaling
preparations)
2. Alignment (includes scaling) including spare
point cloud generation
3. Dense point cloud generation (may be
skipped if a polygon mesh is to be
calculated. However, meshes from dense
clouds are usually superior)
4. Polygon mesh generation (if desired)

5 Journal of Paleontological Techniques

5. Texture generation (if desired)


6. Data export
We provide detailed instructions for the
photography part below. The image editing
required is normally limited to masking and
requires no further explanations. We also detail
the model calculation methods we use as
suggestions for a general workflow. However,
programs change so rapidly that it is highly
recommended to use our methods as a basis
for own experimentation.
We attempt to give all information relevant to
one step of the work process in the respective
section,
which
means
that
information
pertaining to one topic may be spread out
across various parts of the text or repeated.
However, we feel that photogrammetry novices
are better served by this organization, as it
facilitates the use of this work as a take-along
handbook for work during travels.
Equipment list
Essentially,
all
you
need
to
start
photogrammetry is a digital camera and a
suitable computer program. Additionally, a
scale is important because the scientific value
of 3D-data is much higher if the dimensions of
the object are known.
Bare minimum
Digital camera (point & shoot consumer
camera or cell phone)
Object with known dimensions that can
serve as a scale
Travel-suited
DSLR with several lenses, ideally a very fast
zoom lens from wide-angle to moderate
telephoto (e.g., 28-70mm), and a very fast
prime lense (e.g., 50mm 1:1.8). If using a
DSLR with cropped (APS-C) sensor, use a
lens between 28mm and 100mm. Select the
lens based on high sharpness and low
distortion at about f/8 - f/13. Because of the
often difficult positioning of the camera
necessitated by immobile specimens in
exhibits or the field, it can be preferable to
buy a camera with a lower-resolution sensor
but with a rotatable live-view touch screen
that allows shot composition and point-offocus selection by touch (e.g., Canon 650D,
Nikon D5100). For very small specimens a
macro lens or close-up filter is required.
Polarizing filter, which allows reducing
reflections on shiny surfaces - mandatory for
photography in exhibitions with glass covers
(Figure 2).

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 2: Mounted partial skeleton of the thyreophoran dinosaur Edmontonia rugosidens AMNH 5665 in the AMNH
exhibit. The specimen is surrounded by walls and a glass cage. A. Photograph taken without polarizing filter,
camera hand-held close to the glass but not flush with it. B. As in A., but with a polarizing filter and a tripod. Note
how the use of a tripod allowed taking a better exposed and sharper image, and how the polarizing filter weakened
reflections to the point where they can only be noticed on uniform backgrounds.

6 Journal of Paleontological Techniques

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


Tripod (Figure 2), size depending on space
and weight restrictions and specimen size.
For large or exhibition specimens and for
work on laboratory tables a large tripod is
useful. Choose a tripod that allows setting the
camera up nearly on ground level (e.g.
Manfrotto 055XPROB with 804RC2 head) or
bring a second mini-tripod (e.g. Cullmann
Magnesit Copter Tripod with cb 2.7 Ballhead)
so that large immobile specimens can be
photographed at shallow angles.
White and black cardboard or cloth (locally
procured, t-shirts also work) or a greenscreen, and pages of printed text, e.g. a
newspaper.
Folding yardstick with meter scale and 10or 20-centimeter scale bar.
Separate, hand-held flash (not strictly
necessary).
LED-set for lighting specimens from shallow
angle (not strictly necessary); do not forget
to bring multiple-outlet power strip or
several adaptors if traveling abroad.
mid-sized to large mirror (acquired locally,
for photographing immobile specimens that
the camera cannot be placed behind).
On the road, during museum visits or
excavation work, the main factors are
durability, easy setup, space and weight
restrictions.
Special
care
during
the
photography process, in order to achieve high
quality images, is recommended for nonrepeatable situations and objects (e.g., during
excavations). It is always possible to amend
the suggested equipment with gear mentioned
in the lab-setup section (i.e., a remote shutter
release can be very useful, but is not
essential). Museum curators are often willing to
organize materials in advance at the visitor's
cost, so that they are available for the full time
of a collections visit.
Optimal lab setup
DSLR with several suitable lenses (see
above). For the controlled conditions of a
laboratory, the maximum resolution sensor
camera should be acquired for optimal
model resolution. An adjustable camera
stand may be necessary for macro lenses
that do not have a focus ring.
Remote shutter release to avoid vibrations.
Polarizing filter. Allows reducing reflections
on specimens that have shiny surfaces.
Tripod (large and solid) with ballhead for
easy adjustment.
Reflectors.
Flash array (optional).

7 Journal of Paleontological Techniques

Light/LED setup with several rows of focused


LEDs for even lighting of specimens (can be
combined with or used instead of reflectors).
Neutral white/black background (can be
made
from
white/black
cardboard,
professional drapes preferred) or (ideally)
green-screen, and sheets with printed
patterns with human-recognizable features
(e.g., black-on-white text pages or colorful
advertising supplements).
Turntable
(potentially
motorized)
with
featureless cover and degree markings on
the vertical outer surface. Note that
continuous turning is not desirable, so that a
motorized turntable needs to be computercontrolled and stoppable at predefined
intervals.
Glass/perspex cubes of many sizes for
specimen support.
White packing foam (tiny bubbles, so no
points can be found by the program) and
putty for specimen support.
Scales with centimeter and millimeter
markings in various sizes, non-reflective.
A permanent lab setup aimed at rapid and
optimal quality digitizing offers the advantage
that the photography kit can be optimized for
best photograph quality and suitability for
photogrammetric reconstructions, without any
concessions regarding ambient lights or
background.
A key decision to make is whether to use a
flash setup or strong lights. Stronger lights
allow lower ISO values and shorter exposure
times. However, if a specimen is shiny (e.g.,
has been covered with lacquer or has a
crystalline surface) the photographs will show
variations in color or even light spikes from tiny
reflections. In this case, directional light or the
use of flashes can ameliorate or worsen the
problem, thus it is necessary to experiment.
The ideal background for easy model creation is
a green-screen, placed sufficiently far back that
reflected light from it does not fall on the
specimen. Evenly lit it can be selected with a
magic wand tool in the photogrammetry
software or a graphics editing program and
masked/deleted. White or black cloth or even
cardboard can also be used, but it is harder to
light it so evenly that magic wand tools are
effective. However, if the background is
featureless, the photogrammetry software will
not be able to pick up points anyways. The
color of the background, black or white, must
be chosen with the lighting of the images in
mind. A white background for a very dark
(coal) fossil will either lead to underexposure of
the fossil, or white glare around the fossil's

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


edges. In such cases, a black background is
preferable.
As discussed below, for specimens on which
few
features
are
detected
by
the
photogrammetry program, a highly structured
background can be used to improve alignment
at the cost of time spent for masking or
cropping later in the modeling process.
A motorized turntable that rotates continuously
and slowly (then, very short exposure times
are required), or rotates a fixed small angle
and then remains stationary for a short time,
obviates the need of someone stepping and
reaching into the picture between shots.
If very rapid turnaround times are desired it is
possible
to
use
several
cameras
simultaneously. However, achieving even
lighting is then difficult. Currently, efforts are
underway to produce an automated 3D
digitizing line that uses many cameras and
mobile lights for photogrammetry and other
techniques (Santos, 2013). However, this and
similar set-ups are (yet) not sufficiently mobile,
not variable in the optics used and not
affordable for individual scientists' needs.
Legal issues
There are to our knowledge practically no
established practices and rules governing the
use of data derived from photogrammetric
modeling. It is therefore always advisable to
contact the responsible curators in advance and
agree to a bilateral agreement on file
ownership, copyright and file use permissions.
This approach is especially important for
photography conditions that are not covered by
free-use rules, e.g. in collection rooms of
museums.
Additionally, a very important issue is the
automatic copyright transfer included in the
Terms of Use of some (often cloud-based) free
photogrammetry software programs. Use of
such programs should be avoided at all cost,
especially when digitizing specimens owned by
third parties. Such a transfer of ownership is
the reason why we exclude, for example, the
no-fee software 123D Catch.
PHOTOGRAPHY FOR PHOTOGRAMMETRY
The photography phase has an enormous
impact on the final output file. It is often easier
to reshoot a new series of source photographs
instead of trying to save and improve a set of
photos which does not work right away. An
important trick to master is the ability to
visualize, while taking the photographs, the
computer program aligning the photographs, so
that one can plan ahead and find angles that
8 Journal of Paleontological Techniques

potentially were missed. We suggest developing


and following a certain routine in taking the
photos. If possible, all images should be
transferred to the computer right away and a
low-resolution alignment calculated while the
next specimen(s) is/are being photographed.
This allows re-shooting certain images, or
additional photographs to fill gaps, while the
specimen is still accessible and while markers
that were possibly placed on it have not yet
been removed. In difficult scenarios, it may be
necessary to reshoot multiple times for a
suitable model. The quality of pictures is the key
factor for the quality of the final model.
Image formats
Most digital cameras can save photographs in
both an uncompressed, lossless format (usually
a RAW/TIFF version) and a compressed format
(usually JPEG). Agisoft Photoscan and some
other photogrammetry programs can handle
lossless formats. RAW files contain the
maximum amount of information and original
data generated by the sensor and have been
considered the only scientifically justifiable file
format (Verhoeven, 2010). However, we have
found that usually, the artifacts caused by mild
and high-quality compression algorithms, such
as those used for the maximum-size JPEGs in
high-quality DSLR cameras, do not significantly
influence the quality of the alignment or final
model. Similarly, the many image manipulation
options available when using RAW format are
not needed for normal photogrammetric
modeling. On the other hand, RAW shooting
takes more hard disk space, more time, as the
much larger files require longer copying times,
and the photographs may need to be converted
into TIFF images before processing. We
therefore recommend shooting maximumquality JPEGs in normal circumstances.
General rules: ideal photograph quality
Photogrammetry software essentially needs
clean, sharp, evenly lit images; with every
point of the surface of the specimen visible
from at least three angles within the entire
photo set. The task of aligning the camera
positions requires parallax (different positions
and angles) between the images, which for the
creation of panoramic images would be fatal.
Leave out or mask off undesired parts of the
image, either with a green screen during
photography or later in an image editor or the
photogrammetry software. Specific features
which are the highlights of artistic photography
(e.g., dramatic lighting, wide-angle distortion,
selective depth of field) are completely
counter-productive for photogrammetry.

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


Because the quality of the pictures is the key
factor for the quality of the final model,
following these instructions is suggested:
Choose the highest-quality settings your
camera allows. In rare cases, usually on
cheap point-&-shoot cameras, a resolution
lower than the maximum the camera offers
should be chosen, if it offers higher image
quality. In all other cases the maximum
resolution with minimal or without image
compression should be used.
Fill the frame with the specimen, or move
even closer so that each photograph shows
only part of the specimen. The closer the
camera is to the specimen, the higher will
the final resolution of the model be.
However, if too little of the specimen is
visible in each photograph, a large number
of photographs is required, so that the
calculation time and file size become
impracticable and alignment errors between
photographs may degrade the overall quality
of the model.
When photographing immobile specimens,
ignore obstacles hiding part of the specimen
from
view.
As
opposed
to
regular
photography, it does not matter if support
struts or other objects are in front of the
specimen. It is more important to obtain a
good coverage of the entire surface from
many angles than avoiding undesired objects.
Figure 3 shows an example of a photograph
that contains useful photogrammetry data,
but would normally be considered to be of
bad quality.

time and f-stop is a three-way trade-off, in


which the exact best choice depends on the
exact circumstances and specimens.

Every detail that is not in the pictures will


not be in the final mesh. Move underneath
and above the specimen to take photos.
Make sure you have the coverage you need
to get all the details you want, because
reshooting in the exact same conditions is
difficult.
Take in-focus photographs. Focus on part of
the specimen that is in the middle of the
distance range that all the specimens parts
have to the camera. Otherwise, you risk the
close or far end being out of focus. Use a
mid- to high-range f-stop for a large depth
of field and maximum sharpness. This
requires exposure times typically too long
for hand-held shooting, necessitating the
use of a tripod.
Use the middle of the zoom range of the
lens, up to the higher end (which is a
tradeoff with exposure time), to minimize
distortion.
Use
base or low ISO for minimal

Move the camera in relation to the specimen


(or vice versa) to create parallax; do not
take panorama photos (many photographs
from one camera position). The latter can be
acceptable but even small motions of the
camera can drastically improve the quality of
photograph alignment.
Each point on the specimen must be well
visible and in focus on at least two images.
Any point not visible directly will not be
included in the final model (line-of-sight
rule). Take care to point the camera into
recesses.
Take photographs with 40-60% overlap as
rule
of
thumb.
Avoid
near-identical
photographs, including photographs that
differ only in long-axis rotation (i.e. portrait
versus panorama format).
Overview photographs can be supplemented
by close-ups, but much overlap is required.
Take more photographs than necessary,
because unsuitable photographs can later be
excluded from model creation and replaced
by others, and gaps can be closed.

fuzziness/noise. ISO value versus exposure

9 Journal of Paleontological Techniques

Avoid vibrations during exposure (passing


tram, walking around near the tripod during
long exposures, pressing the trigger roughly,
etc.) delay the trigger with the automatic
release, use touch-screen release or remote
shutter release.
Aim for even lighting of the specimen to
avoid shadows, ideally identical in all
photographs. This is especially important for
recesses
and
parts
underneath
the
specimen.
Consciously pick a place to start the image
set, so that you can form a mental picture of
the camera positions and judge if further
images are required. Once you have taken
the first few images, zoom in on the camera
LCD and check the focus and level of noise.
Avoid taking photos against the light
because detrimental light reflections on the
specimen are possible. Do not photograph
into strong lights that can cause lens flare.
Sometimes, when photographing specimens
in exhibitions, it is possible to block
individual lights or reflections by simply
holding a finger or the entire hand in front of
the lens (Figure 3 C). Alternatively, get
another person to help you by holding up a
piece of cardboard.
General rules: photoset suitability

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 3: Mounted skeleton of the ceratopsian dinosaur Protoceratops andrewsi AMNH 6417 in the AMNH
exhibit. A. Photograph taken through the glass cage that contains the specimen, and bears inscriptions on one
side. For a normal photograph, the presence of the letters would be considered inacceptable, but as can be
seen in B., where the features found by Agisoft Photoscan Pro (search target in this case was 10.000 points)
are displayed as dots, the image is well suited for photogrammetry. Grey dots indicate specific features found
for the alignment process, blue dots those used for the alignment. The specimen is in focus and thus delivers
good points, whereas the type on the glass is out of focus and delivers no points. C. Photograph showing
masking of strong reflections on the glass by blocking them with the photographers hand.

Lighting
Even lighting is the key criterion: less light
(especially in combination with a tripod) but
no spotlights can be better than more but

10 Journal of Paleontological
Techniques

uneven light; fluorescent ceiling lights and


white collection cabinets surrounding the
specimen (acting as reflectors) work
surprisingly well!

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


Diffuse lights if necessary (e.g., diffuse the
sun with translucent plastic sheets).
Cardboard (easily bought everywhere) or
white t-shirts for background and as
reflectors to lighten up shadows on the
opposite side and underneath. Aluminum foil
can also work, but beware of possible light
reflexes. Use darker materials for dark
specimens to avoid too much contrast in the
images.
Potentially
use
LED
lights
(easily
transportable, too) from low angle to light
up shadows.
If light conditions are poor and a tripod is
not available or feasible (e.g., wall-mounted
specimens can require work on a ladder),
the exposure time may be too long for sharp
photographs. Consider using higher ISO
values. If all else fails, photography with the
cameras internal flash can produce in-focus
pictures. However, flash-based photography
will always produce strong shadows and
overexposed highlights. It is essential to
avoid shadows and white-outs on a sufficient
number of pictures of each part of the
specimen
to
allow
photogrammetric
calculation. Alternation of the shooting
angles is very important. Shadowed areas
must later be removed from the calculation
in the photogrammetry software, which may
require masking.
Pitfalls
Poor Focus This is the most basic factor to
adjust correctly. Focused parts should ideally
include all important parts of the image.
Wrong f-stop causing poor Depth of Field
Shooting at low f-stop as often happens with
automatic camera settings can cause a
major part of your object to be out of focus.
For the best focus, a stop down between f/8
and f/16 is recommended; above these fstop values, diffraction sets in and reduces
the overall sharpness, rather than increasing
it. Check on internet resources (i.e.,
www.DPReview.com) to find the best f-stop
for certain lenses.
Too few images usually result in bad
alignment, and thus gaps and errors in the
model.
Too little overlap (as above).
Too many images increase calculation time
for no gain. Worse, too many images can
lead to artifacts by grouped alignment
creating two points where there should be
only one. However, it is advisable to take
many photos and use only a selection for
photogrammetry, especially if the specimen
is not at ones disposal.

11 Journal of Paleontological
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Too much overlap, duplicate photographs


(as above).
Highly compressed images contain artifacts
that create false features which will be
tracked by the software. RAW images or
high-quality JPEG are recommended.
Unintended motion of the specimen can lead
to alignment problems if background
features are included in the alignment.
Movement/Motion blur Constantly spinning
a specimen on a turntable while shooting in
burst mode will likely fail because the
shutter speed of most cameras is too slow.
Slow shutter introduces blur in the direction
of the moving object, lowering your effective
resolution. Heavy specimens should be
positioned absolutely stable this is
important if placed e.g. in a sandbed.
Lens distortion The level of distortion in
most normal lenses is no problem for
modern
photogrammetric
software.
However, it is recommended to avoid fish
eye lenses with high barrel distortion.
Changes in lighting (doors opening, the sun
moving, clouds, partial shade under trees,
etc.) can lead to alignment problems and/or
gaps in the model. If a texture is calculated
it can contain artifacts. Moving shadows can
be tracked as false movements and also
affect textures. Static light gives more
consistent
results;
if
feasible,
it
is
recommended to wait for an overcast sky for
outdoor photography.
Strong shadows Dark shadows often do
not work well for point detection because
they
suffer
from
excessive
noise.
Furthermore, the resulting textures are likely
far from realistic colors.
Taking pictures into the direction of a light
source can cause reflections on smooth
surfaces or lens flare, so that no or
erroneous points will be found. At worst,
phantom objects can be caused by lens
flare.
Under-or over exposure A significantly
under- or overexposed photograph loses
usable detail. Inconsistent exposure causes
light and dark patches on the model.
Unequal exposure within image set If the
exposure
differs
significantly
between
photographs it may be impossible for the
program to find corresponding features.
Even if images align well, the following steps
may partly fail, so that the final surface has
artifacts and unrealistic texture colors.
Transparent and shiny surfaces Gathering
data from specimens behind display cases or
shiny surfaces (i.g., caused by lacquer,
liquids, or enamel) is tricky. Current

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


software cannot distinguish between white
pixels on the object and the reflection of
light, as it assumes all surfaces are nonreflective and opaque. Reflections of
surroundings in showcases do not move
consistently with the surface of the object
and the angle of the photo; they may cause
ghost images or holes in the model.
Furthermore, glass surfaces may distort the
objects.
Repetitive features Tracking certain
repetitive pattern, such as architectural
elements in the background, ripple marks on
track surfaces or honeycombs, can cause the
software
to
wrongly
detect
different
instances as corresponding features. Such a
jump can result in strange conglomerate
models with parts of the model presented
repeatedly at different positions.
Featureless
textures

Plain
surface
textures, such as at blank walls or even
dusty surfaces, make feature identification
difficult; the software may fail in rebuilding
depth of the model, or even at building a
model at all.
Very thin specimens If the resolution of
your photos of thin specimens (such as
vertebrate ribs or mollusk shells) is not high
enough, the software-generated point cloud
does not contain enough points to accurately
reproduce the shape of your object. The
points may not be placed in the exact same
place along the length of the thin object.
PHOTOGRAPHING SPECIMENS
Because photogrammetry requires parallax
either the camera or the specimen must move
between shots, or both. Depending on the size
of the specimen and its mobility, as well as the
space available, one of two main methods is
usually adopted: the turntable method, or the
walk-around method. For the former the
camera is usually stationary, ideally on a
tripod. For the latter, the specimen usually
does not move and the camera is moved
around it, either hand-held or on a tripod. Both
methods have their specific advantages and
demands. Only occasionally is it advantageous
to move both the specimen and the camera, for
example when the turntable method is used
with a scale bar that cannot be placed on the
turntable with the specimen.
Aside from choosing between the methods the
image acquisition process is influenced also by
considerations regarding the potential risk of
failure of the in-program model creation.
Photography aimed at optimizing the work
process for the one-chunk model creation

12 Journal of Paleontological
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method described below results in images that,


if the one-chunk method fails, do not make full
use of the superior image alignment capabilities
of the multi-chunk method. We therefore
recommend reading the sections Alignment
methods for more than one set of images
and Background blank or structured?
beforehand.
The turntable method: basic principles
The turntable method has the camera on a
tripod, and a series of photographs is taken of
the specimen on a turntable that is rotated
across a small angle between shots. Figure 4
shows the typical process for photographing a
specimen on a turntable. The photograph series
thus forms a perfect circle of camera positions
around the specimen, with the camera always
aimed at the central vertical axis of the
turntable. In order to cover the surface of a
specimen with a complex geometry it is usually
necessary to vary the height of the camera
position in relation to the specimen by
repeating the process shown in Figure 4 with
the camera at a different height, so that
several concentric circles of photographs are
taken. Undercuts may require additional
photographs, with the camera pointed off the
main vertical axis. These images are usually
created not by moving the camera, but by
manually shifting the specimen on the turntable
and
optimizing
the
position
for
each
photograph. The underside of the specimen has
to be photographed by flipping it over, and
sometimes more than two positions are
required to capture the full surface geometry.
The biggest advantages of the turntable
method are the ability to control the lighting,
photograph speedily, with fixed camera
settings, and the control one has over the
background. The non-turning background must
be as devoid of features as possible or masked,
so that no points are detected on it. Masking is
additional work and should thus be avoided,
but it can allow combining photograph series
from different specimen positions into one
photogrammetric reconstructions without any
need to adjust partial models to each other
(see one-chunk method below), delivering the
highest quality models for the least amount of
fiddling and editing.
The biggest drawback of the turntable method
is, aside from the requirement of a featureless
background, that it requires the specimens to
be mobile, and sturdy enough to be handled.
Additionally, even the sturdiest turntables have
weight limits, so that very large specimens like
sauropod dinosaur sacra or elephant skulls are
too heavy.

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 4: Video showing the basic photography process for specimens that can be placed on a turntable.

Turntable
method
for
small
specimens - using a turntable

mobile

The basic process is shown in Figure 4. Use a


turntable for even lighting and speedy
photography. Heavy-duty turntables for TV
screens cost less than US$30. You may also
use a Lazy Susan, even an office chair that
spins might be sufficient for some objects.
Cover the turntable with a featureless cover
(white/black cardboard) and mark its vertical
outer side at 5 intervals as a visual guide for
the rotation between photographs. If possible,
lift the specimen away from the turntable by
placing it on glass/perspex supports so no
points are detected on the turntable, as its
cover will be out of focus. Use white packing
foam bits to stabilize objects that do not rest
well in desired position.
Take photos at a shallow angle (0-15 from
horizontal) at ~5 to 10 intervals by turning
the turntable. Then, lift the camera higher on
the tripod (30-60); repeat. Then, lift the
camera high above the specimen and take a
few photographs (3 or 4) from ~70-80 up.
The more complex the specimen's geometry,
the more photographs are necessary.
Turn the specimen over (180 if possible, but
smaller angles are sufficient if enough of the
lateral surfaces is captured in each set to

13 Journal of Paleontological
Techniques

combine the two, i.e. if there is good overlap).


Repeat photo procedure as above.
For tiny specimens the use of a high-quality
macro lens or a microscope with digital camera
is recommended. Because such set-ups often
do not allow a large depth of field, it may be
necessary
to
shoot
focus
stacks
of
photographs, i.e. take the same photograph
repeatedly but with a slightly different focus
distance, and use dedicated computer software
to compute these stacks into individual images
(note: the final images should preferably have
EXIF data, which you can add manually).
Turntable
method
for
small
specimens - without turntable

mobile

Use a sandbox or a very sturdy piece of


cardboard as a makeshift turntable (Figure 5).
If this is not possible, use a piece of white
cardboard to blank the table surface (if you
have any), set the specimen on the table with a
scale adjacent, take several photographs from
different positions, then begin the process of
rotating the specimen to complete the picture
set as above. When processing, set in-program
markers for scale on the photos but mask the
scale bar along with rest of the background (if
masking the latter is necessary).

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 5: Digitizing a small specimen (caudal vertebra of Citipati in the AMNH collection) without a turntable. A. Setup with
camera on tripod, light source sub-parallel to camera view and a cardboard box with sand as a makeshift turntable. Printed
paper serves as feature-rich background in case the specimen offers too few features. A caliper serves as scale. In this case,
the specimen offered ample points; see Figures 10 and 11. No markers were put on the specimen due to its fragility; easy
model creation could only be realized using the one-chunk method. B and C. Images from the two series, showing the two
positions the specimen was placed in. Note that a matchbook was used to prop up the specimen in B. All parts of the surface
were still adequately documented in several images, so that the blocking of parts of the specimen from view in some images
had no negative consequences for model creation.

Turntable method: scale bars


The normal procedure for placing a scale bar is
to put it next to the specimen, on the turntable
if one is used, and leave it there for the
duration of the photographing session. If it is
necessary to move the specimen between
photographs that belong to one set, the scale
bar should be removed at this time, or it must
later be masked along with the rest of the
background in all images taken after this time.
A scale bar does not have to be modeled in 3D,
but must at least be present in two
photographs. If it can be exactly marked in
more photographs, the overall accuracy can be
improved. Several scale bars are better than
one, especially for very large specimens of
which each photograph will show only a part,
as they reduce the measurement error. They
should be placed on opposite sides of the
specimen, and can then help reduce distortion.
The larger the scale bar, the better, because
the error caused by photograph resolution
and/or marker placement in the software
becomes relatively smaller. Ideally, scale bars
get rotated with the object.
Even for the one-chunk method, any scale
needs not be in same relative position to the

14 Journal of Paleontological
Techniques

object after flipping over. Theoretically, it is


sufficient that a scale is present and fully
visible in two photographs of one set only, as
long as it does not move relative to the
specimen between them, provided these two
photographs align with the rest of the set.
However, more photographs should be taken to
be on the safe side. Scales should also always
be included in the setup for the second (and
any further) set of photographs, in case the
multi-chunk method must be used if the onechunk method fails (see below).
Turntable method: using physical markers
on specimens
If at least three markers are placed on the
specimen (see Figure 4) so that each is visible
in two photos, the markers can be used to align
models calculated from each of the two (or
more) separate sets of photographs required to
cover the whole surface (required for the multichunk method). It is generally a good idea to
place markers even if the use of the one-chunk
method is intended, as they greatly ease the
task of alignment of parts if the one-chunk
method fails.

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


Because all markers placed on the specimen will
be visible in the final model, markers should be
as small as possible. Tiny pieces of white selfadhesive labels marked with the letter X (use
the crossing point of the two lines for the inprogram marker) and a number (for easier
identification on the photos) work well, if care is
taken that the markers do not fall off when the
specimen is flipped upside down. Make sure to
use only materials from which no chemicals can
leach into the specimen, and which do not leave
any residue when removed.
Markers must be well visible in all positions that
the specimen will be placed in during
photography. It is advisable to turn the
specimen over after placing them, to check if
they really are visible in the alternate positions.
It is possible to produce a marker-free model
with added effort, by taking additional
photographs with the markers removed, and
masking the markers in all photographs. Care
must be taken to take a sufficient number of
images, so that each spot that was covered by a
marker is well represented in sufficient detail in
at least two additional photographs. The markerfree images then provide the surface information
for those parts of the surface that is under the
marker. However, because this approach
involves talking near-duplicate photographs, the
calculation time for the model will rise
significantly.
The walk-around method: basic principles
The walk-around method inverts the roles of
camera and specimen, in that the latter is
stationary, and the former moves. Thus, the
obvious advantage of the walk-around method is
that it allows capturing completely immobile
specimens, as well as those that cannot be
placed on a turntable or manually rotated. The
disadvantages are lack of or limited ability to
control lighting, often a lack of line-of-sight onto
parts of the specimen (especially in exhibitions),
the need to adjust camera settings for each
photograph, and an increased need to construct
a mental image of the sum of camera positions
to judge if the specimen surface has been
sufficiently captured.
Walk-around method: very large or barely
mobile specimens
If a specimen is too large, heavy or fragile to be
placed on a turntable, but can be otherwise
moved (e.g. on a trolley), it is usually advisable
to position it so that there is room to move the
tripod all around it (see Figure 6 for a series of
photographs taken with this method). Also, it is
usually worthwhile to spend some time
searching for a position with good light.
15 Journal of Paleontological
Techniques

Photographs should be taken so that the relative


positions of camera and specimen are roughly
the same as in the protocol for using a turntable
above. The sole difference is that the role of the
stationary part and the mobile part are
exchanged. As a consequence, the lighting,
exposure time and depth of field must be
checked for each camera position separately.
Care must be taken to avoid reflections on the
specimen caused by light sources such as
windows behind it, especially if it is covered by
lacquer. There is no requirement for the camera
positions to be as regularly spaced as the use of
a turntable will usually make them. Figure 7
shows the sparse point cloud, camera positions
and dense point cloud generated from the photo
set shown in Figure 6. Note how several
different elevations of the camera were used to
ensure sufficient capture of the surface.
If additional lights are placed they need to stay
in place during the entire photography, as it is
nearly impossible to reconstruct their exact
positions and directions during later parts of the
photography process. Alternatively, a set-up
producing even light can be moved with the
camera, so that the entire view in each
photograph is evenly lit. Photography should be
conducted rapidly to avoid changing light
conditions. It can be preferable to ignore people
walking through, as they can be masked. In
such an event it is best to take more
photographs.
Specimens too large to be moved at all must be
treated like in situ specimens outdoors, except
for the restrictions imposed by sunlight.
Walk-around method: in situ and exhibition
specimens
Specimens that are immobile can only be
photographed in situ by walking around them as
far as local conditions allow. This places
restrictions on the lighting conditions, and may
mean that parts of a specimen cannot be
digitized because the camera cannot be brought
into positions required to photograph them.
Figure 8 shows an example of a mounted
dinosaur skeleton in an exhibit hall populated by
obstacles in the form of other exhibit specimens.
Especially problematic are specimens outdoors,
where one is dependent on weather conditions,
and often has no access to electrical power
available. Try to avoid strong sunlight as it
causes high contrasts with dark shadows (also
true in exhibition spaces with natural light, such
as the AMNH dinosaur halls); use reflectors/flash
to brighten them up. A light but uniform cloud
cover is preferable. Avoid shooting during times
of day where the sun shines at a shallow angle
onto the surface of interest (i.e., for subhorizontal surfaces prefer shooting during mid-

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


day, for strongly inclined surfaces choose times
accordingly).
When a specimen is subject to changing light
conditions, work rapidly to minimize the

differences and ignore people walking through


view (they can be masked out; take more
photographs to ensure that all parts of the
specimen are sufficiently captured).

Figure 6: Image
set of specimen

Khaan mckennai
IGM
100/1127
(currently stored
at AMNH) on a
trolley, set up in
the middle of the
room so that
there was space
to move a tripod
around
the
specimen.

16 Journal of Paleontological
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Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 7: Model of specimen Khaan mckennai IGM 100/1127 (currently stored at AMNH) created from image set shown in
Figure 6. A. Sparse point cloud and camera positions. B. Dense point cloud in same oblique view as A. C. Dense cloud, medium
density. D. Closer view of the skull. Note the regular arrangement of cameras in A caused by the identical tripod height for
several sets of photographs, and note the height lines in the dense point cloud.

Mounted skeletons, long trackways and similar


very large and complex objects can be
calculated in chunks and merged later (see
below). If this approach is chosen, the
photography should be adjusted by shooting
series of pictures of parts, with markers for the
later alignment placed beforehand. Each part
should contain its own scale bar, as large as
possible. It is for example possible to measure
railings
or
other
architecturally
defined
distances. You may also use a complete
measuring tape or, otherwise, place a yardstick
(ideally at least 2 m) next to each section of the
specimen in a stable position while you
photograph
it.
To
facilitate
correct
photogrammetric
calculation
of
repetitive
pattern such as ripple marks on trackways,
place uniquely colored/shaped objects (e.g.,
clothes, tools, etc.) around the specimen.
Typically, specimens with complex shapes in
exhibition settings suffer from uneven lighting
caused by top-down light or spotlights, causing
strong shadows on the undersides of individual
elements.
Ground-mounted
spotlights
sometimes ameliorate this effect, but are
normally insufficient to allow straightforward
digitizing. If possible, ask for access outside
normal visiting hours, and for the exhibition
lights to be turned off. Many museums have

17 Journal of Paleontological
Techniques

cleaning light that more evenly lights the


specimen. Use reflectors and additional light
sources, and use a flash if nothing else helps. A
second, hand-held and automatically triggered
flash can also be helpful. If nothing else works,
block spotlights or reflections with your hand
(Figure 3C).
The actual process of photography consists of
moving around the specimen and taking
photographs. As simple as this sounds, there
are a number of pitfalls. First of all, it is
important to retain enough overlap between
images, especially if the view of the specimen is
edge-on. Here, it is even more important than
in the turntable method to shoot more images
than one believes to be necessary. Care must
be taken to not shoot panorama series (in
which the camera is pointed in different
directions but remains stationary), as these
image sets have little to no parallax between
individual images.
For huge
specimens,
especially those too large to fit entirely in each
photograph, e.g. because it is impossible to
gain enough distance or because a higher
resolution of the model is required, it can help
to place visual markers of used positions on the
ground, e.g. small pieces of paper, so that one
can keep an overview of what has already been
photographed.

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 8: Four views (A. anterior, B. lateral, C. top, D. oblique) of sparse point cloud and camera positions of an image set of
the torso of the Museum fr Naturkunde Berlin Diplodocus mount in the Dinosaur Hall. Note how the neighboring Giraffatitan
and Dicraeosaurus skeletons have also been captured, and how they block line-of-sight to the right side of the Diplodocus
mount (gaps in camera positions at the top of C). Also, the other specimens and the pedestal they rest on require variations in
the distance between camera and specimen. Note how the tails and necks of the mounts are badly represented in the sparse
point cloud, because they are captured only on the fringes of some images. In this example, erroneous feature matching leads
to sub-optimal alignment, causing increasingly visible distortion with increasing distance from what roughly is the focal point of
the image set (the torso of Diplodocus), especially notable on the right lateral sides of Dicraeosaurus and Giraffatitan in the top
view C.

Exposure must be checked and adapted for


each photograph, as differences can easily
cause color differences which make feature
matching difficult for the program, degrading or
failing alignment. It may even be necessary to
adjust the white balance between shots. RAW
format photographs, in which settings can be
developed later, can be useful under these
circumstances. Especially outdoors, but also in
indoor places with low-mounted light sources, it
is important to avoid casting shadows on the
specimen.
Also, it is often difficult to capture the top
surfaces of huge specimens sufficiently from
ground level. In this case, arrange for a ladder
and a second person to steady it. Long
telescopic masts, the use of kites or UAVs
(Unmanned Aerial Vehicles; e.g. Watts et al.
2012; see http://www.mikrokopter.de) are
useful while photographing large areas.
Walk-around method: specimens behind
glass
Museum
specimens
on
exhibit
behind
glass present an especially difficult case for

18 Journal of Paleontological
Techniques

photogrammetry, because typically the glass is


not perfectly clean and reflects lights and welllit structures (Figure 2A). These reflections
interfere with model creation. Often, a
polarizing filter can remove most of the
reflections (Figure 2B). Placing the camera very
close to (ideally almost touching) the glass and
careful observation of the focus point usually
makes the dust and grime layer on the glass
invisible on the photos (Figure 2B). At worst, a
separate flash held at an acute angle (combined
with a camera placement very close to the
glass) can be used to reduce the relative
strength of reflections, by lighting the specimen
so much that the reflections are outshined. One
also may use optically dense materials like a
hand or a piece of dark cardboard to block
reflections (Figure 3C).

Walk-around method: scale bars


The normal procedure for placing a scale bar is
to put it next to the specimen and leave it
there as long as the photographing session

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


takes place. If it is necessary to move the
specimen between photographs that belong to
one set, the scale bar should be removed at
this time, or it must later be masked along with
the rest of the background in all images taken
after this time.
Walk-around method: using mirrors
If it is physically impossible or impracticable to
place the camera behind the specimen, e.g.
when a specimen is mounted close to a wall, it
is sometimes possible to place a mirror behind
it. Photographs can then be taken of the
specimen in the mirror, and later treated like
any other photograph in the model creation
phase. The same approach can be used for
photographs from below. Make sure to take a
sufficient number of photographs with sufficient
overlap to those taken without the use of a
mirror so that alignment is possible. Because it
is not always possible to fill the frame with only
the mirror additional masking of photographs
may become necessary.
It is not necessary to mirror photographs taken
using a mirror in a photograph editing program
before they can be used in photogrammetry. A
mirror simply re-directs light, so that the
calculated camera position is the hypothetical
location from where the camera would see the
object as it is shown in the photograph.
Background blank or structured?
The background behind and especially under
the specimen has a profound influence on the
model building phase. If the program detects
features on it, these points can be used in the
alignment of the photographs, where they
often play a helpful role because of the large
parallax-induced motions they experience
between photographs. The features will result
in points being created in the dense point
cloud, and accordingly polygons in the polygon
mesh. As such points and polygons are
typically not desired and must be cropped, a
feature-rich background and support for the
specimen typically means an increase in work
time. Alternatively, the background must be
masked by hand in all photographs, taking
often even more time. For specimens on a
turntable features on the background make
masking mandatory as they otherwise impede
the alignment process.
A blank and out-of-focus background means no
masking or cropping is necessary and makes
the one-chunk method easier to use, but may
decrease the chances of a successful alignment
within a set of images. Therefore, the effort in
time
and
money
necessary
to
mask
photographs must be weighed against the
19 Journal of Paleontological
Techniques

effort of re-shooting a specimen for which


modeling fails. If a specimen is accessible only
during a special occasion, or if the cost of reshooting is high due to travel costs, we
recommend using a structured background that
can help with alignment. On the other hand,
easily
accessible
specimens
should
be
photographed using a blank and out-of-focus
background. The example shown in Figure 5
shows the use of a structured background,
because the cost of another intercontinental
trip far outweighs the effort of masking about
2000 photographs taken during the visit. In
fact, the vertebra shown in Figure 5 aligned
well using the one-chunk method, but other,
smaller vertebrae from the same series
required the use of background features for
alignment.
A background that allows easy distinction of
features by a human, such as a page of printed
text (easily available anywhere), also allows
the manual placement of markers to aid the
alignment process, and is therefore better than
a feature-rich but difficult to assess wild
pattern.
Photography tips & tricks
Do not use a camcorder
Although photogrammetric models can be
calculated from video frames, it is not
recommended because motion blur does not
permit crisp images and reduces the quality of
the resulting model.
Easier photography with a tilt screen
A DSLR with a rotatable (touch-) screen and
live view that shows the view of the lens before
the shutter is pressed (e.g. Canon EOS 650D;
Nikon D5100) makes it simpler to choose the
best focal point, and allows speedier and easier
photography in cases where the camera has to
be held very high or low, or over a barrier.
Keeping photograph series apart
Sorting the thousands of photos from a single
session is most easily achieved by using the
large thumbnail folder view. In order to identify
each series of photographs speedily, it is
advisable to write down the first and last image
numbers, or to photograph before and after the
series a piece of paper with the specimen
number and potentially other useful information
(i.e., back set, part 1, etc.) as shown in
Figure 4. This paper can be held in front of the
camera when it is mounted on the tripod, so no
time is lost altering the camera position. The
text should be written with a dark marker thick
enough to be readable in the file explorer
thumbnail view.

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


When series are separated into sub-folders,
these photographs should be moved with them.
IN-PROGRAM WORK
Selecting images
Review and remove bad and redundant images
because too many photos may overwhelm the
software.
Select
only
high-confidence
information for processing. If the background
interferes with alignment, mask it out. Also,
even when using the multiple-chunk method, it
is often faster and easier to mask the
background than to remove erroneous points
from the finished model.
If the alignment is not correct for a certain
image, re-set and re-run or delete it. Human
brains are still smarter at filtering than the
software. Check the camera position display
(e.g., Figures 7, 8 - all camera positions are
fine, and Image 9 - three positions are
obviously faulty) for images that were
supposedly taken 'inside' the specimen, from
below the floor, or from unrealistic distances.
Photograph sets taken with the turntable
method should align in perfectly regular circles,
and images taken at identical tripod heights
must be on one level.
Also, if the set contains many photographs,
consider using only a subset for the model.
Using more images not only increases the total
calculation time, but can also lead to artifacts
on the surface. If images are redundant, tiny
and unavoidable inaccuracies in alignment will
lead to the program finding several points with
minimal differences in position where there
only should be one point. As a consequence,
the surface can become wrinkled, may contain
pyramid artifacts caused by individual points
floating just above or below the rest of the
surface, or may even be created as two subparallel instances.
If a project is very large it can be a viable
alternative to split it into chunks (see below).
Each chunk should contain images that overlap
well. For example, if a mounted skeleton of an
elephant is to be modeled, one chunk could
hold the skull, neck and front limb images,
another the hind limbs, and a third the main
body. Once the images within each chunk are
aligned, the chunks can then be aligned via
markers (see below).
Scaling the model
Scaling needs to be done manually, because
the methods suitable for paleontological
digitizing usually do not allow the use of

20 Journal of Paleontological
Techniques

targets with scales that the software can


recognize automatically. Therefore, at
least
one object of exactly known length must be
visible in at least two of the photographs of one
set, and may not move relative to the specimen
between the two images. It is important that
the two ends of the known distance can be
found with ease on the photographs. Therefore,
measuring a distance on the specimen is not
recommended, unless it is between two tiny
discrete marks. For example, the 'maximum
length' of a bone cannot be used because it will
be nearly impossible to identify the two
measuring points down to one pixel in the
photographs. We recommend using printed
scale bars or (folding) yard sticks marked in
centimeters (practically all photogrammetric
software
uses the metric system). It is
usually best to place in-program markers on
the images, not the 3D model or dense point
cloud.
1. Create one marker at one end of the scale
object and place the same on a second
image.
2. Create a second marker at the other end of
the scale object and place the same on
another image. Note that it is not required
that both the first and second marker are
created on the same image, nor is it
necessary to use the same second image for
placing the second instance!
3. Use the two markers to create a scale bar.
4. Set the length for the scale bar.
5. Repeat for as many scale objects as are
available.
Note that in Agisoft Photoscan Pro the scaling
step can be prepared before the Alignment, but
can also be performed after the images have
been aligned, via the Update option.
Masking
Undesirable parts of photographs containing
moving objects or repetitive background
features cannot always be avoided. Such areas
need to be made unavailable for feature
detection; otherwise they can ruin the
alignment and model creation processes.
Masking can be performed in several ways: in a
graphics program, where the area can be
blanked (any uniform color will do) manually by
painting in or lassoing, or automatically using a
magic wand tool. We have found, however,
that a very uniform background suitable for use
of a magic wand tool usually is so constant that
it does not allow the photogrammetry software
to pick up features anyway, and thus needs not
to be masked. The second option for masking
is
the
in-program
masking
of
the
photogrammetry program.

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 9: Top view of sparse point cloud and camera positions calculated from an image set of Dimetrodon mount at the
Royal Belgian Institute of Sciences, Brussels. Camera positions that are nonsensical (inside the mounts skull) or a massive
mismatch to the images (almost in touch with fore- and hind limbs) are highlighted in red.

In both cases, the exact separation of desired


and undesired data is important. There is a
natural tendency to draw the mask so that all
parts of the specimen are retained in the unmasked area. The direct consequence is that
the contact area between the specimen and the
background is in smaller or larger parts also
contained in the allowed area, and will be used
by the photogrammetry software. However,
there is no 100% clear distinction of the 'this
pixel is specimen, the next one is background'
kind. Therefore, drawing the masking line this
way will have pixels included in the alignment
and model creation that contain information
that is not strictly speaking part of the
specimen. Usually, if the rim of included
background and contact area pixels is narrow,
the effect will be minimal, and amounts only to
a small number of erroneous points floating
close to the main model. In the end, it comes
to a tradeoff between time spent masking and
time spent removing artifacts from the dense
point cloud. However, it is easy to avoid the

21 Journal of Paleontological
Techniques

creation of these points by simply masking the


border area with the background, i.e. by
leaving only those parts of the image unmasked that show only the specimen (Figure
10). Similarly, dark shadows on the underside
of specimens can also be masked, resulting in
more realistic textures, provided there is
sufficient
overlap
within
the
remaining
photograph parts.
If features on the background are needed to
achieve good alignment of the images, it is still
recommended to mask a thin strip of pixels
around the specimen, especially in places
where the specimen contacts the ground. This
strip will later result in a gap in the dense point
cloud that makes cropping the undesired
background points easy and fast.
Alignment
Although running the alignment can be as easy
as simply choosing the corresponding step in
the program menu, there are settings that can

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 10: Image of a caudal vertebra of the oviraptorine dinosaur Citipati osmolskae IGM 100/978 (currently stored at the
AMNH). A. Masked image. Note that the markers used for scaling the model can be in the masked area. B. Points marking
detected features in the image. Note how no features are detected in the masked areas

22 Journal of Paleontological
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Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 11: Model creation process with the one-chunk method on the example of a caudal vertebra of the oviraptorine
dinosaur Citipati osmolskae IGM 100/978 (currently stored at the AMNH). A. Aligned images and sparse point cloud. Each blue
rectangle shows one reconstructed camera position with the matching image filename. Note that the two circles of photographs
are not sub-parallel to each other, as the geometry of the specimen did not allow rotating it by ~180. However, all parts of
the surface are sufficiently captured to deliver a complete model. Two markers were used to set scale (see Figure 10). B.
Closer view of the sparse point cloud with 127,994 points. Because of extensive masking in all images there are no points
representing the background. C-D. Dense point cloud with 5,733,491 points with (C) and without (D) color. E-G. Polygon mesh
with 7,108,439 vertices and 14,216,842 polygon faces with color (E), shaded (F) and wireframe display (G). H-K. Polygon
mesh reduces to (H) 1,500,018 vertices and 3,000,000 polygon faces, 500,012 vertices and 1,000,000 polygons (I), 50,006
vertices and 100,000 polygons (J) and 5,000 vertices and 10,000 polygons (K). L. Photograph of the specimen.

have a strong influence on the quality of the


resulting calculation.
The regular approach should always be the use
of the highest quality alignment the program
offers. However, if this approach fails, it is
recommended to use a low-quality setting
initially, eliminate the images that are
obviously
mis-aligned,
and
re-run
the
alignment at high quality. Similarly, the
number of points the program is supposed to
use for the alignment can be increased at the
cost of much longer calculations times.
Increasing the number per image three- to

23 Journal of Paleontological
Techniques

five-fold can, however, rescue data sets that


otherwise do not align at all. Lastly, choosing
generic pair-selection (if available in your
software) can also help to achieve better
alignment.
Additionally, it is always worth checking the
points display for all images (Figures 3B and
10B) to see if erroneous points are being used
in the alignment. Such points can be on parts
of the image that should not be used, e.g.
background that was insufficiently masked, or
can be on parts of the image that should be
used but produce false-positives in the search

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


for identical features. Typical for the latter case
are points on building parts or other repetitive
structures in the background, or points on
repetitive features on the specimen itself. The
former can be avoided by masking, the latter
can be ameliorated by the method described in
the next paragraph.
The last resort, when a photograph set that
finally fails alignment cannot be easily retaken, consists of adding in-program markers
manually to some or all images that align well
with each other and to all images that do not
align well, and re-run alignment. Depending on
the reasons for the non-alignment this method
can sometimes lead to perfect alignments for a
tolerable amount of work, or can require
several dozens of markers to be placed on
hundreds of images, a task that is usually
impractical. In this case it may be a viable
alternative to split the project into chunks, and
use markers to align the chunks.

Alignment methods for more than one set


of images
Method 1: one-chunk (preferred). Summary
of photography method suitable for onechunk method: One set of photographs on
turntable, flip specimen over, take second set.
Repeat until the entire surface is well
represented in the photograph sets. Include
scale bar in each set. Try to make background
unsuitable for detection of points: use
featureless materials, distance specimen from
turntable (place on perspex cube; cover
turntable with white cardboard; covering with
white or black cloth possible but may have
enough structure to give points). Set depth of
field
so
that
full
specimen
but
not
background/turntable is in focus. Blank or outof-focus background can make masking
unnecessary.
See Figure 11.
1. Add all sets of photos to one chunk,
including the photograph that separates the
two sets. Make the latter unavailable for
alignment; it only serves as an easy clue in
the photo list to distinguish the two sets.
2. Add markers to the scale bar in one or both
sets, create in-program markers and the
scale bars and set the appropriate lengths.
3. Mask
the
entire
background
in
all
photographs, including the scale bars (those
parts of the background on which no points
can be detected can be omitted from the
masking). The more accurately the masking
outline follows the specimen outline, the
better the final model will be and the fewer
erroneous points will be created along the

24 Journal of Paleontological
Techniques

edges of the model (this step may be


unnecessary if no points are found on the
background. Run a test alignment with a low
number of photos and a high point detection
number to check).
4. Align the photos, optimize for all scale bars
as described above.
5. Generate a dense point cloud. This point
cloud should then be inspected for erroneous
points along the areas where the model is
based on one set of photos; typically, this
area features some dark points that pertain
to areas outside the specimen, and stem
from erroneous points found in the shadows
the specimen cast on the table. If the masks
in the photos reach very close to the
specimen, there will be few such points.
Small numbers of erroneous points can
however be ignored as their influence in
polygon mesh creation is negligible.
6. Generate the polygon mesh.
If the one-chunk method fails, use the multichunk method on the same photographs. Only
if this method also fails will it be necessary to
take more photographs.
Method 2: multiple-chunk. Summary of
photography method suitable for multiplechunk method: one set of photos (with or
without turntable), flip specimen over, take
next set (repeat if necessary). Include scale bar
in each set. For walk-around method of large
specimens: Take one set of one end of the
specimen, take a separator photograph, take
set of next section, ensuring that the two
sections
overlap.
Repeat
if
necessary.
See Figure 12.
The multi-chunk method allows using the
background for the alignment step within each
chunk (those parts of the background that do
not move relative to the specimen during the
photography of one set of photos), thus it is a
good method for specimens where few points
for alignment will be found on the specimen
itself. A background well suitable for point
detection should be chosen (newspaper,
Persian rug, etc.). Also, using the multi-chunk
method means less care is needed to set up
the turntable than for the one-chunk method,
and the preparation in the photogrammetry
program is easier, as background blanking or
masking is not needed. However, much fiddling
may later be necessary to adjust the alignment
between the two chunks, or the fit between the
two model halves. The method also makes
handling very large projects easier, by reducing
the overall calculation time and improving the
chance at good alignment. The method works

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 12: Model creation process


with the multi-chunk method on the
example of a fibula of a sauropod
dinosaur from the Utah Field House
of Natural History State Park
Museum in Vernal. A. View of the
program
interface
of
Agisoft
Photoscan Pro with (left) the chunks
1 and 2 containing the two image
sets. Note that markers have been
added to both sets. Markers called
X 1, X2 and X 4 in both chunks
mark the positions of the physical
markers on the specimen, as seen
on the display of the image (right).
Additional
markers
(point
1
through point 4) in chunk 2 are
intended for the creation of scale
bars. B. From the additional
markers (circled in red) four scale
bars have been created (circled in
orange), and their lengths set. Via
the wizard wand button on the top
left an existing alignment can be
refined to include the scaling
information. Alternatively, the scale
bars
can
be
added
before
alignment. In this case, the sparse
point cloud for chunk 2 is shown on
the right. C. The two chunks have
been aligned based on the markers
with identical names, and merged.
The new chunk merged chunks
contains all images and all markers
(green circle). Note that the merged
sparse point cloud shows slight
alignment problems on the lower
left edge of the bone shaft near the
two markers X 4. However, the
near-perfect
alignment
of
the
markers, so close that in the model
view they differ by less than three
pixels each, shows that each
individual set of images was wellaligned
(otherwise
the
3D
placement of the makers would not
fit the other set). D. Dense point
cloud computed from the merged
sparse point clouds. Note that there
are a number of artefacts around
the edges of the bone, but that the
overall shape of the bone and most
details
are
well
represented.
Compare C to Figure 13.

25 Journal of Paleontological
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Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 13: Sparse point cloud from the same image sets as in Figure 12, but computed with the one-chunk method.
Comparison to Figure 12 C shows that the one-chunk method here results in a large number of alignment problems. The most
obvious resulting erroneous points are circled in red.

with more than two series of photos and shells


as well, but more parts usually mean more
trouble aligning them.
As in the one-chunk method, it is possible to
mask the background for a cleaner model
provided the features detected on the specimen
itself suffice for alignment within each image
set. In the example shown in Figure 12 this is
the case; but barely: several images are not
entirely correctly aligned (visible by the handful
of floating points in the lower left quadrant
next to the bone shaft; caused by slight
misalignment of several images). If the same
data set is run via the one-chunk method, the
alignment is less good (Figure 13).
In order to ameliorate the fiddling necessary to
align the chunks, it is advisable to mark the
specimen with points that can be used to place
markers with high accuracy (Figure 12A). Three
markers are the minimum necessary, more are
advisable. However, the markers will be visible
in the texture of the finished model. If two
separate dense point clouds are generated and
later combined in a different CAD program,
there typically will be artifacts from a sub-

26 Journal of Paleontological
Techniques

perfect fit of the two halves and a lot of manual


correction is needed.
1. Add each photograph series to a separate
chunk in one overall file.
2. Add markers to the scale bar in one or both
sets, create the scale bars in the program
and set the appropriate length. Note that the
markers used to create the scale bars should
have different names in each chunk, as they
will otherwise be included for a markerbased alignment.
3. Mask in all chunks only those parts of the
background that move relative to the
specimen, or mask the full background if you
expect the specimen to deliver sufficient
features for alignment.
4. Align the images in all sets (use batch
process).
5. Place markers on the photographs on the
physical markers you put on the specimen.
Rename the markers so that the markers
corresponding to the same physical marker
have the same name in all chunks. Leave
one physical marker unused; it can later be
used to check the chunk alignment.

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


6. Align
the
chunks,
marker-based.
Alternatively, align them point-based, if all
background in all photos has been masked.
7. Merge the chunks.
8. Add a marker to the previously unused
physical marker in two photographs, and
check its position in all other photographs. If
there are systematic divergences, one chunk
is not well aligned. Note that such
misalignment may be obscured on the
model!
9. Remove background points in the sparse
point cloud of the merged chunks.
10. Calculate the dense point cloud.
11. Remove any remaining background points
from the dense point cloud.
12. Calculate the polygon mesh.
Very
large
specimens
(trackways,
excavations, mounted skeletons). The
calculation time for alignment, dense cloud
generation and mesh creation increases
exponentially with the number of photographs
used. If the vast majority of photographs
overlap with a significant portion of other
photographs nothing can be done to accelerate
the process. If, on the other hand, each
photograph overlaps only with a handful of
others, as is the case if a long sequence of
photographs documents a large area such as a
trackway, the set can be split into chunks that
each calculate quickly. If the alignment is
performed in chunks, these can later be
merged based on markers, as described above
for the multi-chunk method, which takes little
time. To ease this task it is useful to place
numbered markers before the photography.
Tracks, for example, may be photographed
with scale bars next to them and a piece of
paper carrying a number. Later, distinct points
on the scale bars can easily be used to create
in-program markers for chunk alignment.
Additionally, for large numbers of photographs
it is usually worthwhile to turn on generic pair
selection which filters out those photos that
likely overlap for alignment and discounts all
other photo pairs, thus reducing the calculation
time significantly.
For dense point cloud and polygon mesh
generation it is similarly advisable to select
only a section of the entire model, calculate the
dense cloud and mesh, save to a new file name
(e.g., the name of the entire file with _part01
appended), select the next part, calculate the
dense cloud and mesh and save with a new
name (_part02), and so on (Figure 14).
Alternatively, in the program the box used for
selecting
the
volume
for
dense
cloud
computation can be moved ahead by dragging

27 Journal of Paleontological
Techniques

a corner point from the beginning of the model


past the points marking the end of the first,
already calculated dense cloud part, so that the
borders between dense clouds are an exact
touch without any gap or overlap. This process
results in manageable file sizes, but each
partial dense cloud is aligned with all others,
and most research tasks can be performed by
alternately using the individual files.
In order to scale large models at high accuracy
it is best to include markers at the far extremes
of the specimen and measure their physical
distance in the field with a measuring tape. For
aligning several versions of models based on
photograph series from different times, e.g. to
document the advance of an excavation and
the relative position of bones removed at
different times of the digging season, or even
across several seasons, it is advisable to place
several immobile and clearly visible markers
(e.g. chisels or poles cemented in drilled
holes).
If large complex specimens were photographed
in chunks, the multi-chunk method described
above can also be used for alignment. For
segmented specimens (e.g. skeletons) it is
advisable to calculate the dense point clouds
for the separate chunks after alignment, as
editing is much faster when done on smaller
overall point clouds. Instead of merging all
chunks (step 7 above), the chunks can be kept
separate and only the finished polygon mesh
models of the individual segments should be
combined into one file, usually in the separate
CAD software used for further processing.
Using
remote
effectively

computing

facilities

If remote computing is available, it can speed


up the calculation of photogrammetric models
considerably. However, not all processes during
the creation of a 3D-model are equally suitable
for remote computing. It is recommended to
finish all CPU-heavy steps (alignment, dense
point
cloud
generation,
polygon
mesh
generation) on remote, while all interaction
heavy steps involving a lot of data loading
(masking, marker placement, point cloud and
mesh editing), and thus on a remote computer
a lot of data transfer, should be carried out on
a local computer.
Additionally, for all programs offering batch
processing, it is advisable to set up batch
operations that run autonomously, e.g.
overnight. Although sometimes steps have to
be repeated later, e.g. because the program
does not automatically set crop parameters
appropriately for dense point cloud calculations,
the avoidance of idle time is usually a

Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE

Figure 14: Trackway of a theropod dinosaur in the Wesling Quarry in Mnchehagen, Germany. A. Oblique view of sparse point
cloud and camera positions calculated from 86 images. B. Roughly top view of sparse point cloud. C. and D. show piecemeal
creation of meshes of only the key areas. In C the area around a single footprint has been selected for mesh generation
(denoted by red points), in D the selection area has been shifted to the next footprint. E. Rhinoceros 5.0 (McNeel Associates;
www.rhino3d.com) view of all separate meshes. Note how the separate meshes are all to the same scale and in correct relative
position to each other, although a complete dense point cloud or mesh of the entire trackway was never calculated. The total
file size (as Stanford PLY) of all tracks is under 100 MB, whereas a mesh covering all of them together would be over 1 GB in
size before cropping. We estimate the time saved at about 70% compared to calculating one single huge mesh and cropping it.

28 Journal of Paleontological
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Mallison and Wings, 2014: PHOTOGRAMMETRY IN PALEONTOLOGYA PRACTICAL GUIDE


significant gain in overall work speed. If
available, a save-after-each-step option should
be used. It allows interrupting calculation of
large batches with minimal loss of completed
work.

Tips & Tricks


Specimens that are flat are best not placed on
the two flat surfaces, because each set of
pictures then captures the flat surface
perfectly, but the area with high curvature
connecting the flat surfaces is usually captured
(and thus reconstructed) less well, with little
overlap between the two photograph sets. It is
therefore advisable to place the specimens on
edge on a support (e.g. on modeling clay;
remember to use a plastic film so that no
chemicals from the clay contaminate the
specimens), so that the flat surfaces are
vertical. When the flat surfaces face the
camera, large angles can be covered between
photographs; whereas the edge-on positions
require small intervals (<5). This setup
creates large overlap between the two picture
sets showing the flat areas, ensuring excellent
alignment and model creation.
Specific, irregular shaped objects, such as
dinosaur ulnae, tend not to rest in two
positions that are roughly 180 from each
other. In such cases, it is advisable to take
three or more sets of photographs, using the
minimum number of positions the bone can
easily be placed in. Both the one-chunk and the
multiple-chunk method can be used, but it is
always worth the extra trouble to take
photographs suitable for the one-chunk
method, as the time invested in aligning many
chunks in the many-shell method is usually
significantly higher.

REFERENCES CITED
Adams, T.L., Strganac, C., Polcyn, M.J., and
Jacobs, L.L. 2010. High resolution
three-dimensional laser-scanning of the
type
specimen
of
Eubrontes
(?)
glenrosensis Shuler, 1935, from the
Comanchean (Lower Cretaceous) of
Texas: Implications for digital archiving
and
preservation.
Palaeontologia
Electronica, 13.3.1T:111.

29 Journal of Paleontological Techniques

TL; DR (SUMMARY)
Taking photographs for photogrammetry can
be a complicated process. As long as you keep
the following fundamental ideas in mind, your
work will benefit:
Decide first how to deal with specimens that
you
need
to
move
to
photograph
completely: either aim to have the
alignment performed only on the features
found on the specimen
blank the
background, or use a highly structured
background useful for alignment
add
markers on the specimen so you can align
partial models easily.
If re-shooting a specimen later will be
difficult or costly, always add a structured
background and markers.
Add a scaling object (scale bar, markers with
known distance on object, etc.).
Take in focus, well-lit photographs with as
high-quality a camera as you can get.
Cover all the surface of your specimen with
much overlap between photographs.
Mask thoroughly (if appropriate for your
alignment and model building method).
ACKNOWLEDGMENTS
Financial support to OW was provided by the
Europasaurus-Project.
Funded
by
the
Volkswagen Foundation. HM received funding
from the Deutsche Forschungsgemeinschaft
(Project SCHW 1452/3-1), and thanks Matteo
Belvedere (MfN) for extensive help in perfecting
photogrammetric techniques and for a presubmission review. We especially thank Stuart
Pond and Mathew Wedel (as reviewers) and
Peter Falkingham (as editor) for very helpful
comments on the initial submission of this
manuscript. The Journal of Paleontological
Techniques furthermore acknowledges the
assistance of The Curry Fund of the Geologist's
Association for the publication of this paper.

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Appendix: Photogrammetry in a nutshell A one-page check-list

- Proper lighting: Use a lot of light and make sure it is consistent throughout the photos (avoid flash
photography; if you have no other option, use flash on all photos and make sure all relevant parts are illuminated),
otherwise the calculation might fail. Daylight is good, but indirect light (shade) is better than sunlight and shadows.
Avoid shiny surfaces (lacquer, enamel) which cause reflections; a polarizing filter or dusting the surfaces might help
here.
- Put a scale in the picture. The larger the scale, the better, as it reduces the relative measuring error. Place the
scale so it does not affect the object you need to document.
- Blank the background. Specimens with a blank background require less editing. Especially specimens that need
to be flipped over and photographed in more than one series of photographs to capture the entire surface are much
easier to calculate with a blank background.
or
- Make the background variable. Objects with unique pattern in the background are easier to calculate, because it
helps the program to identify the specific angles. For example, use a colored newspaper underneath smaller
objects.
- Make no changes during photography! If possible, do not have anything move relative to the specimen (e.g., do
not move the scale between shoots, do not put your foot in the frame or change anything in the background).
- Immobile specimens: avoid repetitive backgrounds (architecture), as these may need to be masked later.
- If you need to document objects from all sides, including the surface they rest on, you may want to use marker
points or stickers on certain spots so that you can flip the specimen over and still have identical marker spots
which later make it much easier to stitch the two halves of your 3D-model together, or align and combine the
various chunks that each contain one photograph set. Markers should also be placed if the calculation is intended
to be done in one direct step, because they will be needed if the one-chunk calculation fails to align the
photographs from both sets correctly.
- Depth of field: The more of the specimen is in focus, the easier is the calculation. If possible use a small aperture
(f13 is usually fine) but be aware that you also need a small shutter speed to prevent blurred photos due to
shaking. If possible, use a tripod and switch on the self-timer (2s), to prevent any vibrations, or use a touchscreen camera and trigger the shutter by a light touch on the screen. If a tripod cannot be used, trade ISO for speed
(up to ISO 400 or 800, depending on camera).
- The exposure should be balanced: there must not be any over- or underexposed sections on the photos.
- Use the highest resolution of your camera and put on a low ISO (a maximum of ISO 400 is usually OK with
DSLR, higher ISO, especially in older cameras, will result in lots of noise). Also, if you want a higher resolution 3D
model, move closer to the specimen. As long as photographs overlap significantly, it is not mandatory that each
photograph shows the entire specimen.
- How many photos? Generally, the more images the better. Try to maximize the coverage of the specimen's
surface. Get ca. 50% overlap on the photographs. To be on the safe side, take redundant shoots: Aim for at
least twice as many photos as needed. Remember the line-of-sight rule! Only what is captured on at least 2 photos
will be included in the 3D-model. What is not visible on your photographs will not be in the model; this especially
concerns tricky parts like deep and/or narrow cavities.

Journal of Paleontological Techniques